Archive of PIPSA results

Version 1

This archive contains all results of the PIPSA analysis run in zipped form. It contains the following subfolders:

• apbs: Computed electrostatic potential grids, all log files and similarity matrices for the full protein and all sites.
• pdb2pqr: PQR files: conversion results after processing uploaded PDB files with pdb2pqr
• pdbs: Original uploaded PDB files

The following sites have been analyzed (provided are site center (based on T. cruzi model, Ca of the residue) and the sphere radius):

Blume site: center Ala4; radius 15 Angstrom; Delye/Mitra&Sept site: center Thr239; radius 18 Angstrom; Chu site: center Thr253; radius 13 Angstrom; aGTP site: center Ala140; radius 15 Angstrom; bGTP interface: center Leu248; radius 12 Angstrom; M-loop: center Phe49; radius 13 Angstrom; N-loop: center Leu286; radius 12 Angstrom; Colchicine site: center Met318; radius 17 Angstrom; Pironetin site: center Leu238; radius 18 Angstrom; Vinca site: center Asn329; radius 14 Angstrom

Literature/mutation based sites originally proposed by:

• Blume site: Blume, Y. B.; Nyporko, A. Y.; Yemets, A. I.; Baird, W. V. Structural modeling of the interaction of plant a-tubulin with dinitroaniline and phosphoroamidate herbicides. Cell Biol. Int. 2003, 27, 171–174.

• Delye / Mitra&Sept site: Délye, C.; Menchari, Y.; Michel, S.; Darmency, H. Molecular bases for sensitivity to tubulin-binding herbicides in green foxtail. Plant Physiol 2004, 136, 3920–3932. Mitra, A.; Sept, D. Binding and Interaction of Dinitroanilines with Apicomplexan and Kinetoplastid a- Tubulin. J Med Chem 2006, 49, 5226–5231.

• Chu site: Chu, Z.; Chen, J.; Nyporko, A.; Han, H.; Yu, Q.; Powles, S. Novel a-Tubulin Mutations Conferring Resistance to Dinitroaniline Herbicides in Lolium rigidum. Front Plant Sci 2018, 9, 97.

Drug-binding sites were inferred from reference structures:

• Colchicine site: a colchicine binding site-like region in alpha-tubulin (colchicine binds to beta-tubulin), inferred from Bos taurus structure 4o2b.
• Pironetin site: inferred from Bos taurus structure 5l6a.
• Vinca site: inferred from Bos taurus structure 5j2t.